The eukaryotic tree of life: endosymbiosis takes its TOL

Resolving the structure of the eukaryotic tree of life remains one of the most important and challenging tasks facing biologists. The notion of six eukaryotic ‘supergroups ’ has recently gained some acceptance, and several papers in 2007 suggest that resolution of higher taxonomic levels is possible. However, in organ-isms that acquired photosynthesis via secondary (i.e. eukaryote–eukaryote) endosymbiosis, the host nuclear genome is a mosaic of genes derived from two (or more) nuclei, a fact that is often overlooked in studies attempt-ing to reconstruct the deep evolutionary history of eukaryotes. Accurate identification of gene transfers and replacements involving eukaryotic donor and reci-pient genomes represents a potentially formidable chal-lenge for the phylogenomics community as more protis